Analysis Code from "Tracking single adatoms in liquid in a Transmission Electron Microscope"

Image series analysis code used in "Tracking single adatoms in liquid in a Transmission Electron Microscope" <br> Scripts 1-3 were applied to all videos with common settings. 1_initial_processing - Extracting and tabulating Metadata, identifying frames from the videos where the megnification is not appropriate and cropping. 2_PCA_denoise - Patch based PCA reduction to highlight Mo Lattice - see SI for details. 3_filter_latticevid - FFT filtering and thresholding PCA denoised video. <br> Scripts 4-7 were applied to individual videos with individual settings. Significant parameter tuning was required to get reasonable atomic trajectories. In this example, parameters are set for the video 15.26.Scanning Preview.emi. 4_filter_atomvid - Manual cropping (eg if frame shifted significantly, or frames were out of focus), then FFT filtering and thresholding original video to highlight Pt adatoms 5_driftcorrect - Drift correction of all videos using identified peaks in the PCA filtered output (Mo Sites) 6_lattice_points - Identification and linking of Mo Site trajectories, using PCA filtered video 7_adatom_points - Identification and linking of Pt adatom trajectories, using FFT filtered video <br> Script 8 was applied to all outputs from scripts 4-7. Generated various plots for each video, and initial processing of trajectory data. <br> The final script "compare" with functions contained in "compfunctions" was applied to outputs from 8. Contained advanced processing, and comparisons between trajectories for each video.